GB2576836B - Compositions and methods for multiplexed quantitative analysis of cell lineages - Google Patents

Compositions and methods for multiplexed quantitative analysis of cell lineages Download PDF

Info

Publication number
GB2576836B
GB2576836B GB1915459.0A GB201915459A GB2576836B GB 2576836 B GB2576836 B GB 2576836B GB 201915459 A GB201915459 A GB 201915459A GB 2576836 B GB2576836 B GB 2576836B
Authority
GB
United Kingdom
Prior art keywords
compositions
methods
quantitative analysis
cell lineages
multiplexed quantitative
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Active
Application number
GB1915459.0A
Other versions
GB201915459D0 (en
GB2576836A (en
Inventor
M Winslow Monte
Petrov Dmitri
P Winters Ian
mcfarland Christopher
N Rogers Zoe
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Leland Stanford Junior University
Original Assignee
Leland Stanford Junior University
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Leland Stanford Junior University filed Critical Leland Stanford Junior University
Publication of GB201915459D0 publication Critical patent/GB201915459D0/en
Publication of GB2576836A publication Critical patent/GB2576836A/en
Application granted granted Critical
Publication of GB2576836B publication Critical patent/GB2576836B/en
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/102—Mutagenizing nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1065—Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1079—Screening libraries by altering the phenotype or phenotypic trait of the host
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/86—Viral vectors
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/136—Screening for pharmacological compounds
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biomedical Technology (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biophysics (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Pathology (AREA)
  • Plant Pathology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Medicinal Chemistry (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Epidemiology (AREA)
  • Animal Behavior & Ethology (AREA)
  • Public Health (AREA)
  • Veterinary Medicine (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
GB1915459.0A 2017-04-03 2018-03-29 Compositions and methods for multiplexed quantitative analysis of cell lineages Active GB2576836B (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201762481067P 2017-04-03 2017-04-03
PCT/US2018/025192 WO2018187156A1 (en) 2017-04-03 2018-03-29 Compositions and methods for multiplexed quantitative analysis of cell lineages

Publications (3)

Publication Number Publication Date
GB201915459D0 GB201915459D0 (en) 2019-12-11
GB2576836A GB2576836A (en) 2020-03-04
GB2576836B true GB2576836B (en) 2022-08-10

Family

ID=63672510

Family Applications (1)

Application Number Title Priority Date Filing Date
GB1915459.0A Active GB2576836B (en) 2017-04-03 2018-03-29 Compositions and methods for multiplexed quantitative analysis of cell lineages

Country Status (8)

Country Link
US (4) US10801021B2 (en)
EP (1) EP3607057A4 (en)
JP (2) JP7021791B2 (en)
CN (1) CN110799643B (en)
AU (1) AU2018249444A1 (en)
CA (1) CA3056796A1 (en)
GB (1) GB2576836B (en)
WO (1) WO2018187156A1 (en)

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10801021B2 (en) 2017-04-03 2020-10-13 The Board Of Trustees Of The Leland Stanford Junior University Compositions and methods for multiplexed quantitative analysis of cell lineages
AU2019354390A1 (en) * 2018-10-02 2021-04-01 The Board Of Trustees Of The Leland Stanford Junior University Compositions and methods for multiplexed quantitative analysis of cell lineages
US20220073905A1 (en) * 2018-12-28 2022-03-10 University Of Pittsburgh - Of The Commonwealth System Of Higher Education Methods and materials for single cell transcriptome-based development of aav vectors and promoters
EP4305164A1 (en) * 2021-03-09 2024-01-17 Illumina Inc Analyzing expression of protein-coding variants in cells
WO2024044304A1 (en) * 2022-08-26 2024-02-29 The Johns Hopkins University Crispr-cas9 as a selective and specific cell killing tool

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2011036453A1 (en) * 2009-09-22 2011-03-31 Medical Research Council Methods of analysing homeostatic state in cell systems
WO2012083069A2 (en) * 2010-12-15 2012-06-21 The Board Of Trustees Of The Leland Stanford Junior University Measurement and monitoring of cell clonality
WO2013169917A1 (en) * 2012-05-08 2013-11-14 Cellecta, Inc. Clonal analysis of functional genomic assays and compositions for practicing same
US20150031556A1 (en) * 2012-02-15 2015-01-29 The Translational Genomics Research Institute System and method of genomic profiling

Family Cites Families (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP4220673B2 (en) 1998-07-21 2009-02-04 ミリポア・コーポレイション Polynucleotide containing ubiquitous chromatin opening element (UCOE)
US7238854B2 (en) 2002-04-11 2007-07-03 E. I. Du Pont De Nemours And Company Method of controlling site-specific recombination
US10724099B2 (en) 2012-03-16 2020-07-28 The Broad Institute, Inc. Multiplex methods to assay mixed cell populations simultaneously
WO2016040594A1 (en) 2014-09-10 2016-03-17 The Regents Of The University Of California Reconstruction of ancestral cells by enzymatic recording
WO2016049024A2 (en) * 2014-09-24 2016-03-31 The Broad Institute Inc. Delivery, use and therapeutic applications of the crispr-cas systems and compositions for modeling competition of multiple cancer mutations in vivo
WO2016106295A1 (en) * 2014-12-22 2016-06-30 Dana-Farber Cancer Institute, Inc. In vivo methods for identifying cancer-associated immunotherapy targets
WO2016108926A1 (en) 2014-12-30 2016-07-07 The Broad Institute Inc. Crispr mediated in vivo modeling and genetic screening of tumor growth and metastasis
WO2018031864A1 (en) 2016-08-12 2018-02-15 Board Of Regents, The University Of Texas System Methods and compositions related to barcode assisted ancestral specific expression (baase)
US10801021B2 (en) 2017-04-03 2020-10-13 The Board Of Trustees Of The Leland Stanford Junior University Compositions and methods for multiplexed quantitative analysis of cell lineages

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2011036453A1 (en) * 2009-09-22 2011-03-31 Medical Research Council Methods of analysing homeostatic state in cell systems
WO2012083069A2 (en) * 2010-12-15 2012-06-21 The Board Of Trustees Of The Leland Stanford Junior University Measurement and monitoring of cell clonality
US20150031556A1 (en) * 2012-02-15 2015-01-29 The Translational Genomics Research Institute System and method of genomic profiling
WO2013169917A1 (en) * 2012-05-08 2013-11-14 Cellecta, Inc. Clonal analysis of functional genomic assays and compositions for practicing same

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
Nature Communications (2014) 5 Article No.: 5871 Nguyen 'DNA barcoding reveals diverse growth kinetics of human breast tumour subclones in serially passaged xenografts' *
PERDIGOTO, CN et al., "Distinct Levels of Notch Activity for Commitment and Terminal Differentiation of Stem Cells in the Adult Fly Intestine", Development, (20110928), vol. 138, no. 21, pages 4585 - 4595, page 4586, column 2, paragraphs 2-3; page 4589, column 2, paragraph 1;DOI: 10.1242/dev.065292 *
Stem Cells Translational Medicine (2016) 5 591-601 Selich 'Massive Clonal Selection and Transiently Contributing Clones During Expansion of Mesenchymal Stem Cell Cultures Revealed by Lentiviral RGB-Barcode Technology' *

Also Published As

Publication number Publication date
JP7021791B2 (en) 2022-02-17
EP3607057A1 (en) 2020-02-12
JP2020512817A (en) 2020-04-30
GB201915459D0 (en) 2019-12-11
WO2018187156A1 (en) 2018-10-11
US10801021B2 (en) 2020-10-13
GB2576836A (en) 2020-03-04
CA3056796A1 (en) 2018-10-11
AU2018249444A1 (en) 2019-10-03
US10738300B2 (en) 2020-08-11
US20210062184A1 (en) 2021-03-04
US20180282720A1 (en) 2018-10-04
US20190367908A1 (en) 2019-12-05
EP3607057A4 (en) 2020-12-09
CN110799643B (en) 2023-12-22
JP2022031485A (en) 2022-02-18
CN110799643A (en) 2020-02-14
US20210009992A1 (en) 2021-01-14

Similar Documents

Publication Publication Date Title
HK1244841A1 (en) Methods and compositions for selectively eliminating cells of interest
IL249618A0 (en) Methods and compositions for sample analysis
IL266940A (en) Compositions and methods related to cell systems for penetrating solid tumors
IL263743A (en) Compositions and methods for the depletion of cells
GB2576836B (en) Compositions and methods for multiplexed quantitative analysis of cell lineages
PT3325669T (en) Compositions and methods of rna analysis
HK1244826A1 (en) Methods and compositions for adoptive cell therapy
SG10202100951SA (en) Chemical compositions and methods of using same
SG10202100726XA (en) Compositions and methods for the depletion of cd117+cells
SG10202108763UA (en) Methods and compositions for nucleic acid analysis
EP3389481A4 (en) Methods, compositions, kits and devices for rapid analysis of biological markers
IL268058A (en) Compositions and methods for the depletion of cd137plus cells
LT3263715T (en) Method for transcriptome analysis of single cells
SG10202111266VA (en) Compositions and methods for library construction and sequence analysis
EP3158085A4 (en) Methods, compositions, and devices for rapid analysis of biological markers
IL269334A (en) Improved t cell compositions and methods
EP3445876C0 (en) Single cell analysis of transposase accessible chromatin
EP3526341A4 (en) Compositions and methods for disease diagnosis using single cell analysis
HK1243334A1 (en) Compositions and methods of stimulating and expanding t cells
GB2562858B (en) Method for the cytometric analysis of cell samples
GB201710674D0 (en) Method of utility usage analysis
HK1252710A1 (en) Multiplexed parallel analysis of targeted genomic regions for non-invasive prenatal testing
RS61429B1 (en) Paraffin suppressant compositions, and methods of making and using
IL273252A (en) Compositions and methods for predicting response to napi2b-targeted therapy
SG11202011274YA (en) Chemical compositions and methods of using same